It would be simpler if you posted your project, this way we could answer your question accordingly to how you setup your project.
You normally have some variable in which you keep your global time in seconds, and that you then display as a 00:00 format. In your code, you apparently have a "Minute" variable, as well as a "Second".
Save the time in seconds (all seconds passed since the beginning of the level), and keep the display format as a way to display your time from your "total seconds elapsed" variable.
In the end, it is like a score, a floating number that you display on screen in a meaningful format (00:00).